CEMiTool Report

Module Statistics

    mod_df <- as.data.frame(table(cem_obj@module$modules), stringsAsFactors=FALSE)
    colnames(mod_df) <- c("Module", "No.Genes")
    DT::datatable(mod_df)

Modules - Profile Plot

    if(length(cem_obj@profile_plot) > 0){
        htmltools::tagList(lapply(cem_obj@profile_plot, plotly::ggplotly))
    } else {
        htmltools::h4("Please create profile plots!")
    }

Gene Set Enrichment Analysis

    if(!is.null(names(cem_obj@enrichment_plot))){
        plot(cem_obj@enrichment_plot)
    } else {
        htmltools::h4("Please create enrichment plots!")
    }

    if(length(cem_obj@enrichment) > 0){
        nes <- cem_obj@enrichment$nes
        pv <- cem_obj@enrichment$pval

        colnames(nes)[-1] <- paste0(colnames(nes)[-1], ": NES")
        colnames(pv)[-1] <- paste0(colnames(pv)[-1], ": p-value")

        # join p-values and nes
        enrich_df <- merge(nes, pv, by.x="pathway")

        # reorder columns
        enrich_df <- enrich_df[, c("pathway", sort(colnames(enrich_df)[-1]))]
        DT::datatable(enrich_df)
    } else {
        htmltools::h4("Please run enrichment analysis!")
    }

Over Representation Analysis

    if(nrow(cem_obj@ora) > 0){
        columns <- c("ID", "Count", "GeneRatio", "BgRatio", "p.adjust")
        ora_list <- split(cem_obj@ora[, columns], cem_obj@ora$Module)

        tl <- htmltools::tagList()
        there_is_barplot <- length(cem_obj@barplot_ora) > 0
        for(i in seq(1, length(ora_list)*3, by=3)){
            n <- names(ora_list)[ceiling(i/3)]
            tl[[i]] <- htmltools::tags$h3(n)
            if(there_is_barplot) {
                tl[[i+1]] <- plotly::ggplotly(cem_obj@barplot_ora[[n]]$pl)
            }
            tl[[i+2]] <- DT::datatable(ora_list[[n]][1:max_rows_ora, ], options = list(pageLength=5))
        }
        htmltools::div(tl)
    } else {
        htmltools::h4("Please run over representation analysis!")
    }

M1.A

M1.B

M2.A

M2.B

M3.B

M4.A

M4.B

Interaction Network